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- PDB-1zze: X-ray Structure of NADPH-dependent Carbonyl Reductase from Sporob... -

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Basic information

Entry
Database: PDB / ID: 1zze
TitleX-ray Structure of NADPH-dependent Carbonyl Reductase from Sporobolomyces salmonicolor
ComponentsAldehyde reductase II
KeywordsOXIDOREDUCTASE / Rosmann fold
Function / homology
Function and homology information


alcohol dehydrogenase (NADP+) / alcohol dehydrogenase (NADP+) activity
Similarity search - Function
: / NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Aldehyde reductase 2
Similarity search - Component
Biological speciesSporidiobolus salmonicolor (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.8 Å
AuthorsKamitori, S. / Iguchi, A. / Ohtaki, A. / Yamada, M. / Kita, K.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: X-ray Structures of NADPH-dependent Carbonyl Reductase from Sporobolomyces salmonicolor Provide Insights into Stereoselective Reductions of Carbonyl Compounds
Authors: Kamitori, S. / Iguchi, A. / Ohtaki, A. / Yamada, M. / Kita, K.
History
DepositionJun 14, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 6, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aldehyde reductase II
B: Aldehyde reductase II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,41112
Polymers74,4502
Non-polymers96110
Water14,772820
1
A: Aldehyde reductase II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7066
Polymers37,2251
Non-polymers4805
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Aldehyde reductase II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7066
Polymers37,2251
Non-polymers4805
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.919, 83.444, 148.262
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Aldehyde reductase II / ARII / carbonyl reductase


Mass: 37225.195 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sporidiobolus salmonicolor (yeast) / Plasmid: pUCAR2 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q9UUN9, alcohol dehydrogenase (NADP+)
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 820 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 32% PEG2000 MME, 100mM ammonium sulfate, 200mM sodium acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 28, 2004
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→45.9 Å / Num. all: 61668 / Num. obs: 61668 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 11.4 Å2 / Rmerge(I) obs: 0.078
Reflection shellResolution: 1.8→1.86 Å / % possible all: 99.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MIR / Resolution: 1.8→45.88 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2253841.33 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.233 6247 10.1 %RANDOM
Rwork0.193 ---
all0.197 61668 --
obs0.193 61668 96.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.6099 Å2 / ksol: 0.353829 e/Å3
Displacement parametersBiso mean: 18.5 Å2
Baniso -1Baniso -2Baniso -3
1-3.25 Å20 Å20 Å2
2---0.68 Å20 Å2
3----2.57 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.8→45.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5252 0 50 820 6122
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_improper_angle_d0.77
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.267 1025 9.8 %
Rwork0.214 9420 -
obs--99 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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